Switched Roles
by nosuchthingastoomanyfandoms
Summary: What if Clary was the one with demon blood instead of Jonathan? How would everything have turned out? This idea has been in my head for a while. Please give it a go.
1. Chapter 1

**The Mortal Instruments Fanfiction**

 **SUMMARY: what if the roles were switched and Clary was the one with demon blood instead of Jonathan? How would everything have turned out? Will still have all the characters mentioned in the original series, but obviously things will be different.**

 ***Disclaimer: I do not own anything.**

Prologue

Hearing her firstborn child's cries for the first time had been one of Jocelyn's most treasured memories. She had looked down at her tiny son, who looked so much like Valentine but had her eyes, and smiled like she had never smiled before. Jonathan. It was beautiful name for a beautiful child. She hugged him close to her chest and smiled at her husband.

Valentine smiled back, but there was something in his eyes that Jocelyn couldn't quite pinpoint. There were times when her husband was as easy to read as an open book and other times when it was impossible to predict what he was thinking. This was one of the times when the latter was true. He seemed distracted –almost _disappointed_ –as he looked down at their child.

Throughout the year, Jonathan grew from a happy giggly baby into a happy and giggly –not to mention clumsy –toddler. Jocelyn loved her son with all her heart. She did, however, notice the change in Valentine's behaviour. He seemed secretive, closed off, barely spending time with her, much less Jonathan.

On Jonathan's first birthday, Jocelyn became pregnant again with her second child. She couldn't keep in her excitement. She was going to have a second child, and Jonathan would have a little brother or sister to look after. She was discussing with Valentine what the name of their second child would be.

"Daniel," he'd said almost instantly.

"Daniel," she repeated, testing out the name. It sounded lovely. "I like the name Daniel. But what if it's a girl?" She thought for a while. "Clarissa. If it's a girl we'll name her Clarissa."

Valentine nodded, although Jocelyn thought she could sense his dislike in the name she chose. What was wrong with him?

She found out the answer to that question nine months later. As she held her new daughter in her arms, she looked down and almost screamed out loud. Clarissa had inherited her red hair and countless freckles, but her eyes were completely black with no whites in them at all. She hadn't cried like Jonathan had, like all babies did when they took their first breath.

"What have you done?" Jocelyn had yelled at Valentine as tears streaked down her cheeks in torrents. "What have you done to our daughter? This is all your fault! I knew there was something wrong with you!"

She was not the only one to notice something off about Clarissa. Jonathan, despite his young age, thought there was something different about his new little sister. Her black eyes scared him and he always stayed a good distance away from her.

Finally, Jocelyn couldn't take it anymore and she decided to leave Idris. She was going to leave Valentine and the daughter she thought she would love. And she would take Jonathan. They would leave Idris and escape into the mundane world –far from Valentine and the monster he created through her. Far from the world of Shadowhunters.

 **Hey! I know this is an unusual fanfic but for a while I've been thinking how different everything would have been if Clary was the demon instead of Jonathan. There will still be the same ships as the TMI series, but obviously the way in which they come about will be different. Hope you like it and please review!**


	2. Chapter 2

It had been sixteen years since Jonathan Christopher Morgenstern, now seventeen, had seen his father and younger sister. He'd only been a year old at the time, but there was one thing that he knew he would never forget. Clarissa's eyes, so unlike his, were like black orbs. They had scared him then, and they scared him now. His eyes clouded with sadness as he realised he would never be able to have a sister he could look out for and care for.

Now he lived in New York with his mother, Jocelyn Fairchild. She had refused to use the name Morgenstern and tried to convince him to drop it too, but for some reason Jonathan felt tied to it. He hated his father for what he had done to his little sister, but Morgenstern was still his name. They lived a normal life –a mundane life. Jocelyn had wanted to escape the world of Shadowhunters, and after what had happened to Clarissa, Jonathan couldn't blame her. He himself wanted nothing to do with them.

Little did he know that his life was about to change.

The school bell rang and Jonathan was one of the first out of class. With his bag slung over one shoulder, he raced out. The first person he spotted was his best friend, Simon. They'd been best friends since pre-school and were still friends now nearing the end of high school. One might wonder how the two even became friends. Heck, Jonathan himself was wondering the same thing. Simon was a nerdy kid, with big thick glasses and always wearing t-shirts with corny phrases. He had been bullied quite a bit for having to wear glasses and Jonathan had felt sorry for him. After that, the two were pretty much inseparable. Simon was like the younger sibling Jonathan had always wanted.

"Hey, Jon," Simon waved, grinning. "How are you going?"

"Terrible," Jonathan shook his head, groaning. "I'm going to kill whoever invented Physics."

Simon laughed. "I'm pretty sure that's impossible. It's just one of those things that have always been around, like time. By the way, did you know Isaac Newton was the first person to use Apple?"

Jonathan rolled his eyes and playfully punched his friend on the arm. "That's quite possibly the worst joke I've ever heard."

His phone began to vibrate in his pocket and he pulled it out. He pressed the green 'call' button and pressed it to his ear.

"Hey, Mum," he said. "I'm on my way home now. Did you want me to get anything?" That was usually the case as they tended to run out of food quickly –admittedly that was the fault of Jonathan as he always felt hungry after school.

"No, Jon, don't come home," Jocelyn said on the other end of the line. Her voice sounded frantic. "Whatever you do, don't come home."

"Mum, what's wrong?" Jonathan asked, worry filling his voice. "What's happening?"

"He's found us, Jon," Jocelyn said, her voice barely a whisper. "Valentine has found us." Those words hit me like a punch to the stomach. "Jon, you have to stay away. You have to go somewhere he won't suspect you'll be."

"Mum…"

"I love you, Jon. Don't you ever forget that." And then the line died. Jonathan stared at his phone, suddenly unsure of what to do. His father, who he had not seen in sixteen years, was back. Worry filled his entire body. What was Valentine going to do to his mother?

"Hey, man, you okay?" Simon asked, concerned. "What'd your mum say?"

Jonathan was at a loss. The fact that Valentine was back to do who knows what to his mother scared him. But he couldn't tell Simon. As much as he trusted Simon, his best friend was still a mundane. If he told Simon about the Shadow world, a world he and his mother had been running from his entire life…he wasn't sure how Simon would take it.

"Hey, man, I just realised I forgot to clean my room and my mum's going to get mad when she comes home from work," he lied. "I'll see you later."

Simon nodded, grinning. "You'd better get going then. I heard a mother's wrath is the last thing you want to experience."

Jonathan rushed home. He'd never disobeyed his mother before, but the way she had sounded on the phone…he just wanted to make sure she was all right. From the outside everything looked normal, like it always had when he'd walked home from school. He cautiously opened the door and froze when he saw the messed up state the house was in.

All the picture frames were smashed on the ground, tables and chairs were upturned. There was even a hole through one of the walls. His mother's room was the worst. The door was completely off its hinges and lying flat on the floor, the bedsheets and pillows were torn and splinters of wood from the smashed closet lay scattered all over the floor.

"Hello, Jonathan." Jonathan swung around and when he saw who had spoken his jaw dropped in surprise. A girl stood in front of him. She was a year younger than him, with fiery-red hair and freckles covering her face. She was almost a splitting image of his mother. Only her black emotionless eyes told him she was his demon-sister.

"Clarissa?" he asked.

"Hello, brother," Clarissa smiled, although the smile held no emotion. "My, you _do_ look a lot like Dad, don't you?"

A sudden rage filled Jonathan that he couldn't quite explain. "What are you doing here?"

Clarissa faked a look of mock-hurt. "Am I not allowed to meet my own brother? Dad sent me here. He's got Mum. Don't worry, he won't hurt her. She's much too important to him. He wants me to bring you to them."

"Stop it," Jonathan shouted. "Stop talking as if we share the same parents. Valentine isn't my father and you aren't my sister. My sister is dead. Valentine killed her sixteen years ago when he fed my mother demon blood."

Clarissa did not look at all offended. Jonathan supposed he shouldn't be surprised, as she did not seem to feel anything at all. She simply continued to smile.

"In time," she said in a cold voice, "you will learn that what Valentine did was the best gift he could ever give me."

And with that she vanished into thin air. As soon as she did, three people burst into the room. They were all teenagers. Two of them looked about his age –one boy and one girl. The other boy looked a bit older. They froze when they saw Jonathan. Looking at the ink-black stuff drawn on their skins, Jonathan knew straight away that these three were Shadowhunters.

"Oh, sorry," the girl apologised. "We mistook this house for another one. We'll just leave now." They thought he was a mundane. He knew he swore to have nothing to do with the Shadow world, but somehow being mistaken for a mundane by Shadowhunters ticked him off.

"There's no need to pretend," he said. "I know you're all Shadowhunters."

The three of them froze and turned to stare at him. They glanced at each other, unsure how to respond. "Are you a Downworlder?" the boy with golden hair asked.

Jonathan shook his head. "I'm a Shadowhunter."

"Where are your runes?" the dark-haired boy asked sceptically.

"I never got them," Jonathan said, maybe a bit harsher than he intended. "My mother and I swore we would have nothing to do with the Shadow world. We were living like mundanes. So why are you here?" The last part he had added sourly.

"Well, our Sensors and Isabelle's necklace went crazy when we passed by this house," Golden boy drawled. "Why wouldn't you want anything to do with Shadowhunters? Mundies are so boring."

"That's hardly any of your business," Jonathan said, disliking the boy's arrogant tone.

"Where's the demon?" the girl, Isabelle, asked. "We know there's a demon. Our Sensors and my necklace wouldn't have gone off otherwise."

"It's gone," Jonathan said, thinking of Clarissa. "You won't find it here anymore."

The dark-haired boy nodded, sensing that Jonathan was telling the truth. "Very well, we'll get out of your way. I'm Alec, by the way. Alec Lightwood. This is my sister Isabelle, and Jace."

"Jonathan," Jonathan said.

Jace seemed to raise an eyebrow, but quickly turned to Alec and Isabelle before he could be sure. "Before going back to the Institute, could we get a snack from Taki's? I'm starving."

Alec and Isabelle rolled their eyes and the three of them disappeared.

Jonathan whipped out his phone and dialled the only other person he knew he could trust. "Luke? Luke, Valentine's back."

 **Hey, here is the next chapter. Hope you enjoy it and please review!**


	3. Chapter 3

**LUKE'S POV**

Not a moment after hanging up the phone, Luke jumped into his truck and drove to the house he so frequently visited under several occasions. Under normal circumstances, he would have taken the time to enjoy the ride –enjoy the normalcy that living like a mundane brought.

But not now. Jonathan's frantic words kept repeating themselves over and over in his head. _Valentine was back_. In his entire life, he had not met a person he hated more than that man. Valentine, his former parabatai, who wanted to rid the world of all Downworlders like him so that the Earth would be "pure". Valentine was the reason for a lot of terrible things, but the one thing Luke knew he would never forgive that man for was how he never gave Jonathan and Clarissa the chance to experience what a real family was like.

Clarissa. Luke sighed sadly when he thought of the beautiful girl Jocelyn's second child could have been. He thought of how wonderful a sister to Jonathan she would have been had she not been poisoned by demon blood. Valentine had ruined any chance for Clarissa to ever become that person before she was even born.

Arriving at the house, Luke burst through the door and immediately stopped in his tracks. To say the place was "trashed" would be to underestimate the state of the house entirely. He heard footsteps and brought his hand behind his back and gripped the hilt of his knife tightly, but he relaxed when he saw it was only Jonathan.

 **JONATHAN'S POV**

Seeing Luke brought a wave of relief washing over Jonathan. He was holding Jocelyn's stele which he'd found amongst the rubble, miraculously intact. He was fingering it gingerly, unsure of what to do. He knew of runes, but he didn't actually know any, and so the stele was pretty much useless to him.

"Luke," Jonathan said, trying to keep his voice from shaking. "Luke, Valentine has my mother. I don't know where he took her but…"

Luke rested a hand on his shoulder gently. "Don't panic," he said. "We'll find your mother, I promise. I know someone who can help."

At first, Jonathan wondered who Luke was talking about. Was there really someone they could trust with what just happened? And then it dawned on him.

"Magnus Bane," he said, and Luke nodded.

Magnus' place was not far from the house –well, not as far as Jonathan had thought. It was about an hour's drive if you obeyed the speed limits, which Luke did not. The warlock's house looked about average, although if Jonathan looked hard enough he could see it was nowhere near the average mundane house. Luke parked the truck and got out. Jonathan made to unbuckle his seatbelt too, but Luke stopped him before he could exit the passenger door.

"Jon, I think it's best if I go in first alone," he said.

"Why?" Jonathan asked, somewhat indignantly. "It's just Magnus."

Luke nodded. "That is exactly the reason. You know Magnus. He always has to bargain if we want something from him. And since your mother and I know him on a personal level, I might be able to negotiate a lower price in return for his help."

Jonathan slumped back in his seat. "Fine," he grumbled.

Luke nodded and walked up to the front door.

"Interesting." Jonathan jumped in shock and swivelled his head to find Clarissa lounging in the front driver seat beside him. "Why would you, a Shadowhunter, want help from two Downworlders?"

"How did you get in here?" Jonathan asked. He was sure he never heard the car door open.

Clarissa grinned at him. "I have my ways. You know, I did promise Father I would bring you to him. Of course, it would be so much more convenient if you came voluntarily. It would be less, ah, messy that way."

Jonathan balled his fists. "Well you can tell Valentine to get stuffed. I'm done with him. Can't you see what he's done to you?"

Clarissa clicked her tongue in annoyance. "That's no way to speak of our father. And like I said, he's given me the best gift in the world." She looked like she wanted to say more, but her gaze went to Luke and Magnus, and then back to her older brother. "Well, until next time, brother," she said cheerily and then disappeared.

"I look forward to it," Jonathan muttered sarcastically.

 **MAGNUS' POV**

Ever since he had stepped foot inside, Magnus had been staring incredulously at Jonathan. The kid looked so much like Valentine –from his white-blonde hair to the way he stood. Jonathan resembled his father in almost every way possible. Except for his eyes, of course. Jonathan had Jocelyn's eyes –safe gentle green eyes, the precise colour of spring grass.

Magnus turned away from the mini version of Valentine and turned instead to Luke. "I've contacted the New York Institute. They'll be here soon."

"Institute, you say?" Jonathan spoke up. "They mentioned an Institute."

"Who?" Luke asked.

"Alec, Isabelle and Jace."

Magnus raised an eyebrow. "You know them?"

"They came to my house shortly after…after I did," Jonathan said. Magnus frowned suspiciously. The boy seemed to be hiding something. "They said their Sensors went off as they passed by my house. We didn't really talk much. I admit, I wasn't very welcoming." He seemed to have no shame in that. But then, that would be expected if you had been avoiding the Shadow world all your life. "Why are they coming here?"

"Well, I don't know about _them_ , exactly," Magnus said. "But I was hoping Robert and Maryse Lightwood would arrive soon." He exchanged a glance with Luke, the unspoken passing between them. Both the Lightwoods –and Luke himself for that matter –had been a part of Valentine's Circle back when they had been young and naïve, before they found out Valentine's true intentions. Magnus knew Luke had left; or rather he'd been kicked out, after he had been Turned into a werewolf.

There was a knock on the door and Magnus went to answer it. He saw Robert and Maryse standing out there, looking at him expectantly. "You called us, Magnus?" Robert said. "You said that Valentine had returned?"

Magnus nodded. "I did. Come in. We have much to discuss."

As soon as Magnus shut the door, Maryse gave a loud gasp and her hand flew to her mouth. "Valentine," she breathed, staring at Jonathan.

Jonathan did not look happy with being mistaken for his psychopathic father, but when he spoke his voice was surprisingly calm –and somewhat snarky. "No, sorry, Valentine's not here. If you want I can pass on a message to him for you."

"Jonathan," Luke said, sounding tired. "Now is no time for joking around."

Magnus couldn't help grinning to himself. Jonathan may seem more like Jocelyn in personality, but it seemed some of Valentine's sarcasm had been passed onto his son. Some things just never change within families. He should know.

Robert had taken one look at Jonathan and made a scowl –albeit a subtle one that only Magnus was able to detect. Maryse, on the other hand, was still staring wide-eyed at the white-blonde-haired boy who resembled so much of the father he hated. It was funny, really, how Jonathan could look so much like Valentine, and yet not be like him at all.

Magnus cleared his throat. "Right," he said. "Now that we're all here and Jonathan has finished with his not-so-funny joke, we can get straight to it. As you are all aware, Valentine was here and he took Jocelyn with him…"

 **JONATHAN'S POV**

Jonathan sat at the back of the Lightwoods' car, not daring to even open his mouth to speak. He still did not understand why he couldn't just stay at Luke's. He'd spent his entire life running from Shadowhunters, wanting nothing to do with them, and now he was being forced to live with them. Robert and Maryse didn't look back at him or speak to him until they reached the New York Institute. It was huge –so much so that he vaguely wondered how the mundanes could walk past without stopping to gawk at it.

"Welcome to the Institute," Maryse said in a somewhat stiff voice. Jonathan knew she still looked at him and saw the man she thought she could trust. He didn't like it, but he knew it was true.

Robert opened the door, but said nothing –as if he was trying to look anywhere but at Jonathan.

"Alec, Isabelle, Jace, Max!" Maryse called.

There was a scuffle of feet and then four people appeared in front of them. Three of them Jonathan recognised as Alec, Isabelle and Jace –the three teenagers who had appeared in his house earlier. The fourth was a young boy who looked about seven, although he had an air about him that made him seem older.

"Hey," Jace said, eyes widening in surprise. "You're the weird guy who didn't like Shadowhunters and would rather live among mundanes. What are you doing here?"

Alec rolled his eyes and Isabelle punched him on the arm. "Really, Jace?" she said. "Why do you never think before you speak?"

Jace grinned. "Just because. I think it proves my honesty."

Maryse cleared her throat. "This is Jonathan Morgenstern, and he'll be staying with us from now on."

"Morgenstern?" Alec repeated, his eyes widening. "As in, Valentine Morgenstern's son?"

Jonathan couldn't help it. He was tired of people judging him by his psychopathic father whom he hated with a passion. "Yes, I am Jonathan Morgenstern and yes, my father is Valentine Morgenstern. And for the record this is the last place I want to be right now. My mother and I swore we would have nothing to do with the Shadow world after what happened to my sister."

As soon as he realised he had mentioned Clarissa, he instantly regretted it. He didn't know why, but he felt he should keep the secret of his demon-sister. He didn't like the idea of people asking questions –questions he had no idea how to answer.

There was a long silence that followed his rant. It was as if the Lightwoods hadn't been expecting him to say that. Robert and Maryse were staring at him, wide-eyed and their mouths slightly open. Alec, Isabelle and the young boy, who Jonathan guessed was Max, looked down at the ground, suddenly interested in their shoes.

Jace, on the other hand, was staring at Jonathan curiously. He had a look on his face that Jonathan could not quite figure out. His brows creased together slightly and his head tilted to the side.

Jonathan took a deep breath. "Sorry, I didn't mean to blurt out everything like that. Can I just have some time on my own?"

Alec, Isabelle and Jace showed him to what would be his new room. Jonathan shut the door behind him and lay down on the soft white covers, completely exhausted from the long day. Within seconds, he had drifted into an uncomfortable sleep.

 **Hey, here is the next chapter. Thanks for the wonderful and encouraging reviews. I will try to follow the basic storyline of CoB, but there will obviously be a lot of differences due to Clary being the evil one in my story instead of Jonathan. However, in this story Jace's backstory is pretty much the same as in the original series –with maybe a few minor differences. As I probably said before, there will still be Clace (although obviously differently set out), Sizzy and Malec.**

 **Oh, and of course the characters will keep their sass!** **Anyway hope you enjoy and please review!**


	4. Chapter 4

_Jonathan watched as Clarissa navigated the windy underground tunnels quickly, as if she had been growing up here all her life. Jonathan wondered if she actually had. The place certainly seemed fitting –it was about as dark as his sister's soul, he thought bitterly, if she had one. She came out into a large cavernous room dimly lit by a few small candles. She stopped walking and Jonathan followed her gaze to the centre of the room. He almost let out a loud gasp._

 _Right in the middle of the room was the figure of a sleeping woman, lying still on a bed made entirely of stone. Her chest was moving up and down ever so slightly and her red hair was spread out all around her face._

Mum _, Jonathan mouthed. What had Valentine done to her? What had he done to leave her in this state?_

 _For the first time since he saw her, Clarissa seemed to hesitate. It was as if the sight of their mother filled his sister with an uncertainty that Jonathan would not have associated with a demon at all. Maybe, just maybe, there was still some humanity left in his little sister. She began to walk towards the sleeping form of Jocelyn._

" _Hello, Mother," she said calmly. "Do you remember me? I'm Clarissa, the daughter you abandoned sixteen years ago. I know you can still hear me, and I want you to know that I've come back; me and Father. He wants us all to be together, you know. You and me and him and Jonathan, mostly you. He still loves you; I don't understand how you can't see that. As for me," she scoffed, "I tried to forgive you, you know. I really did. But you never came back. And for that I hate you."_

 _Jonathan watched as the scene unfolded before him. The way Clarissa was talking, even if she had said she hated Jocelyn…Jonathan wondered if –and maybe even hoped –his sister was not completely demon, if there was some small part in her that was still worth loving…_

A loud banging noise woke him up with a jolt and he looked around, momentarily forgetting where he was. And then he remembered the events of the day before. He was in the Institute. Despite his protestations and pleas to stay anywhere but in the home of the people he vowed to avoid, Luke had insisted that the Institute was the best and safest place for him for the time being.

There was the banging noise again. "Jonathan, if you want breakfast you'd better come into the kitchen now," Isabelle's voice came from the other side of the door. "You have no idea how much of a pig Jace is when it comes to food."

Jonathan tried to hold back a sigh. "All right, I'm coming." He sat up and rubbed the sleep from his eyes. His mind drifted back to the dream. Was it even a dream? It had felt so real. He remembered Clarissa's words to his sleeping mother: _I tried to forgive you_. Did she really? Did Clarissa, the terrifying demon she was raised to be, really try to forgive his mother? Valentine had poisoned her blood before she was even born, but was there still some part within her –even if it was tiny –that was still human? Was there a small part in that demon that was the sister he never had?

He shook his head and walked out of his room. He didn't want to think about it. He didn't want to believe there was a still a small sliver of humanity left in his sister. It would be easier to believe she was fully a demon. That way he wouldn't have to feel anything but hatred.

It took him a while to find the kitchen –he was not used to such a large house. The Lightwoods were already eating. They turned their heads when they saw Jonathan walk in. Maryse made a little high-pitched sound and quickly averted her eyes to her plate. Robert's features turned into a scowl before he, too, resumed eating. Alec still looked groggy from sleep, but he waved a greeting at Jonathan. Isabelle gave him a warm smile and little Max waved enthusiastically.

Jace, he realised, was looking at him intently, a slight frown on his face as if Jonathan looked familiar to him. But then he gave a subtle shake of his head and grinned.

"Well, good to see you're finally awake, Jonny."

Jonathan scowled at the nickname. "And I guess you've been up for hours, have you? What, do you spend hours trying to dye your hair golden, Goldie Locks, maybe to look pretty?"

Jace scoffed. "Please, I have no time to do such mundane tasks early in the morning. As if I'd give up my beautiful sleep time for that. And for the record, my hair is naturally blonde."

Alec rolled his eyes. "Jace."

"Yes?"

"Shut up."

Isabelle scoffed. "Boys," she muttered.

Jonathan couldn't help smiling slightly. Maybe living in the Institute wouldn't be as bad as he'd originally thought.

*line break*

In the training room, Alec, Isabelle and Jace were teaching Jonathan a few moves that would be useful in a fight. Jonathan was hesitant at first. He'd never had any use to fight before whilst he was living his mundane life. But he was a quick learner and soon he could last twenty minutes sparring with Alec –although Alec won of course, having more experience with this kind of stuff.

"You know," Alec said. "You're pretty good. Have you ever gone demon-hunting?"

Jonathan shook his head. "I've been trying to live like a mundane, remember? And mundanes don't hunt demons. They can't even _see_ demons."

"Oh, right," Alec said. "Well, we have to take you sometime. It's actually really fun."

Jonathan nodded. "Sounds cool," he said.

"Yeah, but just remember I call dibs on the biggest one," Jace said, grinning. "You babies might not be able to handle it."

"Oh please," Isabelle rolled her eyes. She twirled a small but razor-sharp knife delicately in her hand before throwing it viciously at a target, hitting the bullseye. Jonathan couldn't help but be impressed. "Could a baby do that?"

Jace seemed to look thoughtful for a while, though the way he was tapping his chin made Jonathan realise he was only pretending. "Well, the average baby couldn't. But I bet I would've been able to."

"You're such an arse," Isabelle sighed exasperatedly.

"No, I'm just incredibly talented," Jace grinned.

Jonathan looked at Alec. "Is he always this arrogant?"

Alec sighed. "You have no idea."

 **Hey, I know nothing really happened in this chapter. This is more of a getting-to-know-each-other chapter. I promise there will be more exciting things happening next chapter. Anyway, Hope you like it and please review.**

 **P.S. I just had to add in Jace's famous line where he says he's a natural blonde. I couldn't resist.**


	5. Chapter 5

Jonathan retreated back into his room for a short R&R. He had to admit, training was fun. In fact, if he hadn't known of the evilness that Shadowhunters were capable of, he suspected he'd have loved being a Shadowhunter. _So would Clarissa_ , he thought sadly –the way he always felt when he thought of the little sister he could've had. _Clarissa would have loved it too_.

Grabbing his phone, he realised he had a text message from Simon, inviting him to one of his band gigs on Saturday at Java Jones. Jonathan almost laughed out loud. Java Jones? Hasn't the old coffee shop suffered enough from all those poetry readings? That's not to say he didn't like Simon and his band friends. They weren't horrible, exactly, but they weren't great either. Plus the fact they kept changing their name every week.

But Saturday though? Why did it have to be Saturday? Alec, Isabelle and Jace were bringing him demon-hunting at the Pandemonium. It was his first ever demon-hunting and Jonathan was really looking forward to it. Ugh! Why did Shadowhunters have to ruin his perfectly normal mundane life?

He sighed and typed a reply: _sorry, man, my mum's grounded me for my messy room._

As soon as he pressed the 'sent' button, the guilt gripped at his stomach. He hated lying. But what was he supposed to do? He couldn't just say " _oh sorry, man, but I'm going out with a couple of friends demon-hunting at this club and I may or may not come out of it alive_ ". First of all, Simon would not believe him and would most likely feel hurt because he'd think Jonathan didn't want to go. Secondly, Simon was a mundane. He couldn't just walk up to his best friend and start blurting about the Shadow world.

A moment later his phone vibrated, indicating that Simon had replied: _haha, that's all cool. Man, it sucks to be grounded._

Jonathan chuckled. He realised Simon was his only link to his mundane life. Everything else had been twisted into some sick Shadowhunter version –but not Simon. The little nerdy kid who had become Jonathan's little brother remained stubbornly normal, which Jonathan was glad for.

Just a few seconds after he lay down on his bed and closed his eyes, there was a knock on his door. The door opened and Isabelle's head poked in. Her long dark hair was tied in a ponytail, but there were a few loose strands hanging around her face that had come out during training.

"Jonathan, Mum wants to see you," she said. "She's in the library."

Jonathan nodded and got up, following Isabelle down the long corridor –Isabelle's high-heels clopping loudly on the wooded floor. He grinned. "Tell me you're not going to wear those shoes on Saturday."

Isabelle looked at him, frowning in confusion. "Why not?"

"Why not?" Jonathan repeated incredulously. "You could hear those shoes from miles away. It's sure to attract the demon at Pandemonium."

Isabelle scoffed. "Oh please, you have a lot to learn about our demon-hunting strategy. And besides, I have a very strict policy which I live by."

"And what's that?" Jonathan asked, raising an eyebrow.

"Nothing below eight inches," Isabelle replied smugly.

"What kind of policy is that?" Jonathan asked as they stopped walking. Isabelle only grinned at him and opened the door leading into the library.

The library was huge –but then Jonathan supposed he shouldn't be surprised, as the Institute itself was massive. There were tall bookshelves against the wall holding all sorts of books ranging from modern fiction mundane novels **(yes, I probably just called every other fandom we love mundane…sorry…)** to what looked like large century-old books probably about the history of Shadowhunters or some other stuff about the Shadow world. There was a fireplace to the side basking the entire room in an amber glow. His mouth was hanging open in awe.

"I'm glad you like this room," Maryse said from behind a desk. "Or maybe it's just the sheer size of it that shocks you."

Jonathan spun around. She was holding a book in her hands, although from where he stood he couldn't see the title. From the way she sits, with her posture upright and back slightly arched, Jonathan had no problem believing that this was Isabelle's mum. They looked so much alike. The only difference was that Maryse was looking at him with a look of wariness on her face.

"You wanted to see me?" Jonathan asked, trying to ignore the tight feeling in the pit of his stomach.

Maryse sighed and put her book down. She placed her head in her hands tiredly. "Where to start?" She looked up at him. "I'm sorry."

"For what?" Jonathan blinked, taken aback.

"For mistaking you for your father," Maryse said. "It was not fair of me to judge you by him." She paused, seeming to hesitate. "Valentine was very popular once. Everyone loved him. We were all jealous of his talents. But then everything changed when he attacked the Clave. He was so clever. He managed to trick us into believing his intentions for the future of Shadowhunters were good." She paused yet again and took a shuddering breath. "You look so much like him, although you probably know that already. I was shocked when I saw you at Magnus'. But watching you joke around with Alec, Isabelle and Jace, maybe you are more like your mother."

By the end of it, Jonathan didn't know what to say. Some of the tension in the room had eased, but Jonathan had trouble trying to fully comprehend what was going on. Whatever he had expected Maryse Lightwood to say, an apology would have been at the bottom of his list –though his list was not very long to begin with. He realised she was looking at him intently, as if waiting for him to say something.

"Um…thanks…you didn't really need to apologise for anything," he said.

A slight smile appeared on Maryse's face. "Your modesty is so unlike your father." She paused, chuckling slightly. "Although, at Magnus', I could tell some of his sarcastic wit had been passed to you –and his stubbornness."

At first Jonathan was not pleased to have something in common with his psychopathic murderous father, but he realised Maryse meant it in the best way and he smiled. "If you say so, I will try not to let you down."

*line break*

Saturday night came quickly and Jonathan waited in the hallway with Jace for Alec and Isabelle. Both of them wore the standard black uniform all Shadowhunters wore when they were out to fight demons. Jonathan looked at the plain sword hanging at his waist. He had refused to take any seraph blades, even though they were the weapons all Shadowhunters were expected to have. He'd also refused to be Marked. To take on the standard tradition of all Shadowhunters would be to completely throw away his old mundane life. He wasn't sure he was ready for that.

"What did you say about your sister?" Jace asked, frowning slightly.

Jonathan looked at him. "What? I didn't say anything."

"When you first came here, you said you wanted nothing to do with the Shadow world after what happened to your sister," Jace said. "What happened to your sister?"

Jonathan was silent. _She's a demon_ , he thought to himself. _You're going demon-hunting. Just tell them._ But he couldn't. He didn't know what it was, but he just couldn't tell them. Could it be…no, it can't be. Clarissa is a demon. She's been a demon all her life. But there was still one part of him –one small part –that still looked at her, and saw his sister. There was still a part of him that looked at the evil demon and saw the little sister he never had.

"It's nothing," Jonathan said, not looking at Jace.

Jace looked suspiciously at him. "It doesn't seem like nothing. Come on, just tell me. I swear I won't tell anyone else. What happened to your sister?"

Jonathan shook his head. "Has anyone ever told you you're very annoying?"

"All the time," Jace smirked. "Finally, what took you two so long?"

Alec and Isabelle were walking down the corridor –Izzy's boots, of course, made loud clopping noises that could be heard from a mile away.

"You're kidding right?" Jonathan said. "You're not _actually_ going to wear those boots are you?" Izzy simply smiled sweetly at him.

"Let's go," Alec said, leading the way out of the Institute.

 **JACE'S POV**

Throughout the whole ride to Pandemonium, Jace kept looking at Jonathan. He had a feeling the guy was hiding something. Even if it was something to do with a person Jace had never met before, he had a bad feeling about it. But it wasn't just that. Jonathan looked familiar. Jace thought he remembered someone looking almost exactly like Jonathan, but he couldn't pinpoint the memory.

There was a long line of mundanes waiting impatiently to enter the Pandemonium. They put on their glamours –although Jonathan was reluctant –and snuck into the club. Jace almost laughed out loud at all the ridiculous get-ups the mundanes wore before he remembered he was glamoured so a laugh coming from nowhere would be weird to the mundies.

"Split up," he said, taking charge like he always did on demon-hunts. "But stay close and within sight of each other."

He began to make his way through the crowd, although it was hard because the floor was packed. One girl accidentally bumped into him and the two went crashing into the ground.

"Oh, I'm terribly sorry," the girl said, sounding flustered. "I wasn't looking where I was going."

Jace felt a vibration in his pocket but it stopped almost immediately after. He smiled and helped the girl up. She was pretty, he had to admit. Her red hair fell around her face, although the lighting of the club made it impossible to tell the colour of her eyes.

"That was quite a fall, I must say," Jace grinned. "Although it is a relief to have a pretty girl land on me instead of an ugly guy."

The girl gave a light laugh that sounded like music to Jace's ears.

"I really must know the name of the beautiful girl who pushed me over," he said.

The girl giggled. "My name's Clary. What's yours?"

"Name's Jace. Clary. That's a beautiful name for a beautiful maiden."

Clary laughed. "You flatter me, Jace. Well, I really must go. I'll see you around."

She turned around and when Jace blinked, she was gone. It was only then that he realised what had happened. He had just talked to a mundane…a mundane with the Sight.

And not only that. His Sensor was gone.

 **Hey, I thought I would end this chapter here for a cliffy. Hope you like it and please review!**


	6. Chapter 6

Jonathan wandered through the crowded club. 'Pandemonium' certainly was a fitting name for the place. He'd never been to this sort of thing before. It was, according to his mother, the place for mundanes, Shadowhunters and demons to mix –and it was for this reason that he'd avoided the club. He glanced around. Everyone seemed to enjoy themselves dancing crazily to some weird music Jonathan had never heard before, but none of them struck him as demon-like.

His eyes fell on a blue-haired boy holding what looked like a long stick –although if he concentrated enough he could see it was a razor-sharp weapon of sorts. Narrowing his eyes in suspicion, he began to follow the boy at a safe distance. He gripped his sword tightly, ready to pull it out at any sign that confirmed the boy was a demon.

He felt a hand on his shoulder and turned to see Izzy shaking her head. "Wait," she said. "Let me go first. I'll lead him into the 'NO ADMITTANCE' room and then you, Alec and Jace follow."

Jonathan nodded and held back, but didn't take his eyes off the boy, whom Izzy had just confirmed was the demon. Izzy walked up to the demon and battered her eyelids, smiling sweetly and beckoning with her finger. Alec and Jace appeared beside Jonathan –Jace was grinning like a little kid on Christmas morning.

They watched as Izzy led the demon into the 'NO ADMITTANCE' room. After waiting a few seconds, the three Shadowhunters followed, Alec bringing up the rear and shutting the door quietly behind him.

There was the sound of a loud gasp and the crack of a whip. "Shadowhunter," the demon hissed angrily, his dark eyes full of malice. "I knew you lot were here."

"Maybe you're not as bright as you thought," Jace said, still grinning. "If you didn't recognise Izzy here as a Shadowhunter. Or maybe you were distracted?"

The demon hissed and growled. "I would've been able to tell _you_ were one. You're as arrogant as the rest of them." He continued to glare at them; however his eyes went wide when he turned to Jonathan. "Valentine," he gasped.

Jonathan sighed exasperatedly. "No, sorry, Valentine's not here. Would you like me to pass on a message to him for you?" he replied sarcastically.

The demon regained his composure. "But of course, you are Jonathan Morgenstern. It really is a pity you turned out so weak. Your sister has done us a great service."

Jonathan blinked, taken aback. "What? What are you talking about? How do you know Cl –my sister?"

The demon laughed. "All of us know of her," he said. "She has promised us a place in the higher ranks when she takes over the world."

Jonathan's eyes widened. What? Clarissa was planning to take over the whole world? His _own_ sister?

"I've had enough of you talking a bunch of trash," Izzy growled. "Let's just kill him now."

"I agree," Alec nodded. "It's clear this demon is lying and selling us nothing but crap."

Jace twirled a seraph blade in his hand. He whispered a name and the blade of the knife began to glow brightly. The demon's eyes widened with fear and struggled against his constraints, but Izzy's whip was too strongly wound around him.

Jace plunged the knife into the demon and, with a short yell of agony, it disappeared.

*line break*

When they arrived back at the Institute an hour later, they made straight for the weapons room. As they were taking off their gear, Jace cleared his throat. "I don't suppose one of you have a spare Sensor on you, do you?"

Isabelle raised an eyebrow. "Tell me you didn't lose yours."

"Well if I didn't I wouldn't have asked," Jace said, but he was biting his bottom lip nervously.

"How'd you lose it?" Alec asked.

"I think that girl might have accidentally taken it," Jace replied, somewhat sheepishly. "We bumped into each other accidentally and it might have fallen out of my pocket without me noticing."

"So you were distracted by a pretty girl?" Jonathan smirked. "What was her name?"

"Clary," Jace said. "And I wasn't distracted. She was apologising over and over and I had to tell her everything was cool. She has the Sight by the way…Jonathan are you all right?"

Because Jonathan had gone very pale at the mention of the name. Clary…occasionally he had heard his mother refer to his demon-sister by that. Sometimes he would find her sitting on the floor, a small box lying open in her lap and a small lock of red hair –identical to Jocelyn's but Jonathan knew it was Clarissa's –clasped in between her quavering hands. It was during these times, Jonathan knew, that Jocelyn was thinking of the daughter she could have had –the daughter that could have been Jonathan's little sister. The daughter that died the moment she was born.

"Hello," Jace waved a hand in front of Jonathan's face, jolting him from his thoughts. "Anybody in there?"

Jonathan looked around at Alec, Isabelle and Jace. He wanted to tell them. He really did. But he didn't know what it was that was stopping him. Was he…could it possible he was actually feeling _protective_ of his sister? But why was he feeling this way? Clarissa was a demon. She was unable to feel anything human. She _wasn't_ human. Jonathan barely even knew her –they'd spent so many years apart. And yet…could it just be his brotherly instinct to protect his little sister, even though she was evil? Maybe he was holding onto the small hope that there was still a tiny bit of human left in her, and if he told Alec, Izzy and Jace –who were all demon-hunters –they would try to hunt her down without giving her the smallest chance to be human.

"I need some time by myself," he said, walking out of the weapons room without waiting for an answer.

As soon as he entered his room, he realised there was someone already inside. His eyes widened at the sight of Clarissa sitting on his bed, but she looked different. Her small body seemed tense and she played with her fingernails nervously.

"Well, look who decided to show up," Jonathan said.

Clarissa jumped up off the bed. "Jonathan," she said, her voice for some reason sounding desperate. "Please, I need your help."

"Oh?" Jonathan raised an eyebrow sceptically. " _You_ need _my_ help is it?"

Clarissa bit her lip. "I know you probably don't believe me, and I don't blame you. But please, I don't know how much long this will last."

Jonathan frowned. "What do you mean? How long will _what_ last?"

"This." Clarissa indicated to herself. "This is me, Jonathan, the _real_ me. I managed to gain back some control but…I don't know how long I can do it before…well, you know."

Jonathan didn't know how to respond. He looked carefully at her face, trying to detect any sign that she was lying. His eyes widened when he saw that her eyes were green –the exact same green as his and his mother's. They weren't the emotionless black from before.

"Clarissa?" he said uncertainly. "It…it's really you?"

Suddenly she jumped onto him, wrapping her arms around him in a tight hug. Recovering from his initial shock, he hugged her back. Relief flooded through him. He did have a sister. She wasn't completely gone. He'd always wanted a younger sibling to look after and now, after sixteen long years, he finally had one.

"I'm scared, Jon," Clarissa whispered. "My whole life I've never felt in control of my body. And now I don't know how long I have before…before it takes over again."

Jonathan looked into his little sister's green eyes that were so much like his but held so much fear. "I won't pretend to know what to do," he said gently and reassuringly. "But I know I will do whatever I can to make sure the demon in you is gone forever. Deal?"

Clarissa took a shaky breath. "Deal." She hugged him one last time before heading to the window. Just before jumping out, she looked back at him, grinning. "By the way, Jace is cute." And then she was gone.

 **Hey, sorry if you've been waiting a long time but here is the next chapter. I know this may be a little short, but I hope you like it. And I know it's weird that Clary would be scared and all that, but I really wanted her to have a human side as well because Clary is one of my favourite characters in the original TMI series and so I couldn't make her a completely evil character in my story. Anyway, hope you enjoy it and please review.**


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